def setUp(self):
self.gp1 = GenePart()
self.gp2 = GenePart(feature_type='CDS', indices=[1, 44])
self.gp2.add_indices([65, 103])
self.gp2.identifier = ['foo1', 'foo2']
self.gp2.parent_id = 'mama'
self.gp3 = GenePart(feature_type='exon')
def add_stop_codon(self, indices):
"""Adds a stop_codon GenePart to MRNA.other_features"""
stop_id = self.identifier + ":stop"
stop_parent_id = self.identifier
stop = GenePart(feature_type='stop_codon', identifier=stop_id, \
indices=indices, parent_id=stop_parent_id, strand=self.strand)
self.add_other_feature(stop)
def test_constructor(self):
self.gp1 = GenePart()
self.assertEquals(0, len(self.gp1.indices))
self.assertFalse(self.gp1.score)
self.assertFalse(self.gp1.parent_id)
self.assertEquals('CDS', self.gp2.feature_type)
self.assertEquals('+', self.gp1.strand)
def add_start_codon(self, indices):
"""Adds a start_codon GenePart to MRNA.other_features"""
# TODO figure out naming scheme...
start_id = self.identifier + ":start"
start_parent_id = self.identifier
start = GenePart(feature_type='start_codon', identifier=start_id, \
indices=indices, parent_id=start_parent_id, strand=self.strand)
self.add_other_feature(start)
def test_sort_attributes(self):
gp = GenePart()
gp.indices = [[25, 30], [5, 10]] # out of order!
gp.identifier = ["gp2", "gp1"]
gp.score = [10, 8]
self.assertEquals("gp1", gp.identifier[1])
self.assertEquals([25, 30], gp.indices[0])
gp.sort_attributes()
self.assertEquals("gp1", gp.identifier[0])
self.assertEquals([5, 10], gp.indices[0])
def process_other_feature_line(self, line):
"""Extracts arguments from a line and instantiates a GenePart from them."""
kwargs = self.extract_other_feature_args(line)
if not kwargs:
return
parent_id = kwargs['parent_id']
if parent_id not in self.mrnas:
self.orphans.append(line)
return
parent_mrna = self.mrnas[parent_id]
parent_mrna.other_features.append(GenePart(**kwargs))
def test_gagflagged(self):
gp = GenePart()
self.assertFalse(gp.gagflagged())
gp.add_annotation("gag_flag", "awesome flag")
self.assertTrue(gp.gagflagged())
def test_add_annotation(self):
gp = GenePart()
self.assertFalse(gp.annotations)
gp.add_annotation("gag_flag", "this gene part rulz")
self.assertTrue(gp.annotations)
